Thanks for the replies.

I don't run any background defrag programs, or anything taxing on the resources. No Antivirus or antimalware software Just Rainmeter and driver controllers for the Video and Sound devices.

"when was the last time you did a registry scrub?"
The rig was just built a little over a month ago. Total format and clean installs.

"is your laptop also a radeon chipset? i've noticed the radeon tech doesn't run the game as efficiently."
Yes it is. The funny thing is that it runs the game nearly as well as my desktop. It could even be considered more stable considering that it can run the game in full screen mode without encountering the issues that my desktop does using near identical settings. The only difference would be the screen size.

"From what I can tell, when in full screen mode it prioritizes resources to to FFXIV"
Now that you mention it, when I was trying to find a fix for the problem, I found this little program that someone made called FFXIV Priority Booster. Link. The guy who made it was having a problem that sounded similar to mine. Quoting his post from the link:

Since I have a CPU bottlenecked computer with a Dual Core processor, I felt really bad when I realized that the game itself is really poorly optimized for us dual core users. It spawns so many threads in the process and takes up all my CPU in no time, even if I have a nice GPU (9800GT).

One thing I realized was that the game itself, when in windowed mode, ran at Low Priority. While trying to fix it, setting it to High, it just kept changing it back to Low with no success.

That's where I decided to code an application to help me out with this task, the FFXIV Priority Booster. All I wanted to do is to keep scanning for the process and put its priority to High (or the one selected by the user). While meddling with the code, I realized I could actually do more! I could manage directly the threads, polling the application itself, and try to improve the performances on us poor Dual Core users.

After some days, working on this, analyzing the underlying threads and processes, I was able to come up with this. Some friends in my steam group / Link shell helped me out beta testing and reporting bugs and they all say the applications helps (in a way or another) with their FPS and smooth gameplay.
I tried using it but saw no measurable difference in performance, but then again I'm using a quad core processor. The program does what it advertises though. Keeps FFXIV at high priority (or whatever you set it to) and organizes threads.